AF2χ: Predicting protein side-chain rotamer distributions with AlphaFold2

Abstract The flexibility of protein side chains is an essential contributor of conformational entropy and affects processes such as folding, stability and molecular interactions. Structure determination experiments and prediction tools such as AlphaFold generally fail to capture or represent the conformational heterogeneity of proteins in solution. Experiments can be used to study side-chain flexibility, but cannot be applied at scale, and most prediction methods focus on reconstructing the minimum free energy state rather than an ensemble representing side-chain configurations. Here, we use AlphaFold2 and its internal side-chain representations to develop AF2χ that predicts side-chain χ-angle distributions and generates structural ensembles. We extensively benchmark AF2χ predictions using experimental NMR 3 J -couplings and s 2 order parameters, as well as dihedral angle distributions derived from collections of experimental structures, demonstrating the accuracy of AF2χ in generating accurate side-chain ensembles. We also compare the accuracy of AF2χ with molecular dynamics simulations and recent machine learning models aimed to generate conformational ensembles and show that AF2χ provides state-of-the-art accuracy orders of magnitude faster than molecular simulations. With its speed and accuracy, AF2χ offers a strong complementary option to simulations and rotamer library approaches, making it particularly valuable for applications such as protein design, ligand docking and interpretation of biophysical experiments.